Mehari

Mehari is a software package for annotating VCF files with variant effect/consequence. The program uses hgvs-rs for projecting genomic variants to transcripts and proteins and thus has high prediction quality.

Other popular tools offering variant effect/consequence prediction include:

• SnpEff
• VEP (Variant Effect Predictor)

Mehari offers predictions that aim to mirror VariantValidator, the gold standard for HGVS variant descriptions. Further, it is written in the Rust programming language and can be used as a library for users' Rust software.

Supported Sequence Variant Frequency Databases

Mehari can import public sequence variant frequency databases. The supported set slightly differs between import for GRCh37 and GRCh38.

GRCh37

• gnomAD r2.1.1 Exomes gnomad.exomes.r2.1.1.sites.vcf.bgz
• gnomAD r2.1.1 Genomes gnomad.genomes.r2.1.1.sites.vcf.bgz
• gnomAD v3.1 mtDNA gnomad.genomes.v3.1.sites.chrM.vcf.bgz
• HelixMTdb HelixMTdb_20200327.tsv

GRCh38

• gnomAD r2.1.1 lift-over Exomes gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz
• gnomAD v3.1 Genomes gnomad.genomes.v3.1.2.sites.$CHROM.vcf.bgz
• gnomAD v3.1 mtDNA gnomad.genomes.v3.1.sites.chrM.vcf.bgz
• HelixMTdb HelixMTdb_20200327.tsv

Building from scratch

To reduce compile times, we recommend using a pre-built version of rocksdb, either from the system package manager or e.g. via conda:

# Ubuntu
sudo apt-get install librocksdb-dev

# Conda
conda install -c conda-forge rocksdb

In either case, either add

[env]
ROCKSDB_LIB_DIR = "/usr/lib/" # in case of the system package manager, adjust the path accordingly for conda
SNAPPY_LIB_DIR = "/usr/lib/"  # same as above

to .cargo/config.toml or set the environment variables ROCKSDB_LIB_DIR and SNAPPY_LIB_DIR to the appropriate paths:

export ROCKSDB_LIB_DIR=/usr/lib/
export SNAPPY_LIB_DIR=/usr/lib/

By default, the environment variables are defined in the .cargo/config.toml as described above, i.e. may need adjustments if not using the system package manager.

To build the project, run:

cargo build --release

To install the project locally, run:

cargo install --path .

Internal Notes

rm -rf /tmp/out ; cargo run -- db create seqvar-freqs --path-output-db /tmp/out --genome-release grch38 --path-helix-mtdb ~/Downloads/HelixMTdb_20200327.vcf.gz --path-gnomad-mtdna ~/Downloads/gnomad.genomes.v3.1.sites.chrM.vcf.bgz --path-gnomad-exomes-xy tests/data/db/create/seqvar_freqs/xy-38/gnomad.exomes.r2.1.1.sites.chrX.vcf --path-gnomad-exomes-xy tests/data/db/create/seqvar_freqs/xy-38/gnomad.exomes.r2.1.1.sites.chrY.vcf --path-gnomad-genomes-xy tests/data/db/create/seqvar_freqs/xy-38/gnomad.genomes.r3.1.1.sites.chrX.vcf --path-gnomad-genomes-xy tests/data/db/create/seqvar_freqs/xy-38/gnomad.genomes.r3.1.1.sites.chrY.vcf --path-gnomad-exomes-auto tests/data/db/create/seqvar_freqs/12-38/gnomad.exomes.r2.1.1.sites.chr1.vcf  --path-gnomad-exomes-auto tests/data/db/create/seqvar_freqs/12-38/gnomad.exomes.r2.1.1.sites.chr2.vcf --path-gnomad-genomes-auto tests/data/db/create/seqvar_freqs/12-38/gnomad.genomes.r3.1.1.sites.chr1.vcf --path-gnomad-genomes-auto tests/data/db/create/seqvar_freqs/12-38/gnomad.genomes.r3.1.1.sites.chr2.vcf

rm -rf /tmp/out ; cargo run -- db create seqvar-freqs --path-output-db /tmp/out --genome-release grch37 --path-gnomad-mtdna ~/Downloads/gnomad.genomes.v3.1.sites.chrM.vcf.bgz --path-gnomad-exomes-xy tests/data/db/create/seqvar_freqs/xy-37/gnomad.exomes.r2.1.1.sites.chrX.vcf --path-gnomad-exomes-xy tests/data/db/create/seqvar_freqs/xy-37/gnomad.exomes.r2.1.1.sites.chrY.vcf --path-gnomad-genomes-xy tests/data/db/create/seqvar_freqs/xy-37/gnomad.genomes.r2.1.1.sites.chrX.vcf --path-gnomad-exomes-auto tests/data/db/create/seqvar_freqs/12-37/gnomad.exomes.r2.1.1.sites.chr1.vcf  --path-gnomad-exomes-auto tests/data/db/create/seqvar_freqs/12-37/gnomad.exomes.r2.1.1.sites.chr2.vcf --path-gnomad-genomes-auto tests/data/db/create/seqvar_freqs/12-37/gnomad.genomes.r2.1.1.sites.chr1.vcf --path-gnomad-genomes-auto tests/data/db/create/seqvar_freqs/12-37/gnomad.genomes.r2.1.1.sites.chr2

prepare()
{
    in=$1
    out=$2

    zcat $in \
    | head -n 5000 \
    | grep ^# \
    > $out

    zcat $in \
    | grep -v ^# \
    | head -n 3 \
    >> $out
}

base=/data/sshfs/data/gpfs-1/groups/cubi/work/projects/2021-07-20_varfish-db-downloader-holtgrewe/varfish-db-downloader/

mkdir -p tests/data/db/create/seqvar_freqs/{12,xy}-{37,38}

## 37 exomes

prepare \
    $base/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr1.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-37/gnomad.exomes.r2.1.1.sites.chr1.vcf
prepare \
    $base/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr2.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-37/gnomad.exomes.r2.1.1.sites.chr2.vcf
prepare \
    $base/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chrX.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-37/gnomad.exomes.r2.1.1.sites.chrX.vcf
prepare \
    $base/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chrY.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-37/gnomad.exomes.r2.1.1.sites.chrY.vcf

## 37 genomes

prepare \
    $base/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr1.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-37/gnomad.genomes.r2.1.1.sites.chr1.vcf
prepare \
    $base/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr2.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-37/gnomad.genomes.r2.1.1.sites.chr2.vcf
prepare \
    $base/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chrX.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-37/gnomad.genomes.r2.1.1.sites.chrX.vcf

## 38 exomes

prepare \
    $base/GRCh38/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr1.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-38/gnomad.exomes.r2.1.1.sites.chr1.vcf
prepare \
    $base/GRCh38/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr2.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-38/gnomad.exomes.r2.1.1.sites.chr2.vcf
prepare \
    $base/GRCh38/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chrX.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-38/gnomad.exomes.r2.1.1.sites.chrX.vcf
prepare \
    $base/GRCh38/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chrY.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-38/gnomad.exomes.r2.1.1.sites.chrY.vcf

## 38 genomes

prepare \
    $base/GRCh38/gnomAD_genomes/r3.1.1/download/gnomad.genomes.r3.1.1.sites.chr1.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-38/gnomad.genomes.r3.1.1.sites.chr1.vcf
prepare \
    $base/GRCh38/gnomAD_genomes/r3.1.1/download/gnomad.genomes.r3.1.1.sites.chr2.vcf.bgz \
    tests/data/db/create/seqvar_freqs/12-38/gnomad.genomes.r3.1.1.sites.chr2.vcf
prepare \
    $base/GRCh38/gnomAD_genomes/r3.1.1/download/gnomad.genomes.r3.1.1.sites.chrX.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-38/gnomad.genomes.r3.1.1.sites.chrX.vcf
prepare \
    $base/GRCh38/gnomAD_genomes/r3.1.1/download/gnomad.genomes.r3.1.1.sites.chrY.vcf.bgz \
    tests/data/db/create/seqvar_freqs/xy-38/gnomad.genomes.r3.1.1.sites.chrY.vcf

Building tx database

cd hgvs-rs-data

seqrepo --root-directory seqrepo-data/master init

mkdir -p mirror/ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot
cd !$
wget https://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.files.installed
parallel -j 16 'wget https://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/{}' ::: $(cut -f 2 human.files.installed | grep fna)
cd -

mkdir -p mirror/ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/cdna
cd !$
wget https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
cd -
mkdir -p mirror/ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/ncrna
cd !$
wget https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz
cd -
mkdir -p mirror/ftp.ensembl.org/pub/grch37/release-108/fasta/homo_sapiens/cdna/
cd !$
wget https://ftp.ensembl.org/pub/grch37/release-108/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz
cd -
mkdir -p mirror/ftp.ensembl.org/pub/grch37/release-108/fasta/homo_sapiens/ncrna/
cd !$
wget https://ftp.ensembl.org/pub/grch37/release-108/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh37.ncrna.fa.gz
cd -

seqrepo --root-directory seqrepo-data/master load -n NCBI $(find mirror/ftp.ncbi.nih.gov -name '*.fna.gz' | sort)
seqrepo --root-directory seqrepo-data/master load -n ENSEMBL $(find mirror/ftp.ensembl.org -name '*.fa.gz' | sort)

cd ../mehari

cargo run --release -- \
    -v \
    db create txs \
        --path-out /tmp/txs-out.bin.zst \
        --path-lable-tsv PATH_TO_MANE_LABEL.tsv \
        --path-cdot-json ../cdot-0.2.21.ensembl.grch37_grch38.json.gz \
        --path-cdot-json ../cdot-0.2.21.refseq.grch37_grch38.json.gz \
        --path-seqrepo-instance ../hgvs-rs-data/seqrepo-data/master/master

Development Setup

You will need a recent version of protoc, e.g.:

# bash utils/install-protoc.sh
# export PATH=$PATH:$HOME/.local/share/protoc/bin